... balance ...
Hmm... Here I'll admit that I feel a little out of my expertise (this isn't really my genre), but what imbalance would result from aliens as equals?
... graphics (the portrait of the planetary governor *must* be a human ) ...
Since this is an empire, not a democracy, the emperor (or someone in the hierarchy of the empire) presumably appoints governors. Thus simply have governors be appointed from within the imperial hierarchy, which is based on the player's homeworld, and governors will (presumably) always be human.
Also I do not want the AI to assimilate player's population.
Why not?
Also your original race is a soft cap to conquest (only terrans can crew your military ships - you can't conquer aliens and then make them into soldiers to conquer even more of their brothers & sisters).
Hmm... I suspect that this could be solved in other ways.
One thing that comes to mind is that inducting a planet into the empire would presumably take manpower--governors, soldiers on the ground, builders, translators, etc--thus reducing your available manpower. This could be countered by conscription from the new planet--but a species that has just been conquered might balk at more than light conscription, and thus be more likely to rebel.
Another idea might be to make the aliens physiologically incompatible with human ships, and their ships (if they have them) be unsuitable for expanding the empire (perhaps lacking faster-than-light capability).
[edit]
Yet another thought: it occurs to me that a planet that has just been conquered has likely just had its military crippled; on top of that, its economy and population (and especially that portion of its population trained for combat) may have taken a significant hit. Thus such a planet might not be in a position to immediately offer conscripts for the empire's armies, only slowly recovering--at which point its recovering population growth could simply be modelled with the terran and alien population conflated, and the question of the composition of starship crews might never come up.